Director Kirby Dick and producer Amy Ziering share details from their documentary, "The Invisible War," which looks into the thousands of rapes and sexual assaults in the military. Wes Moore joins the Morning Joe panel to continue the conversation.

In “The Invisible War,” a new documentary on sexual assault in the military, service people repeatedly share a version of the same story. Subject after subject describes a harrowing assault, the intimidation and retaliation that often followed, and the failure of an institution to hold perpetrators accountable for their crimes.

“It was uncanny, chilling and disturbing,” Amy Ziering, a producer for the film, told msnbc.com. “I would do interview after interview and these women who never met each other and served in different branches would tell almost identical stories.”

Last year, 3,192 sexual assaults, from unwanted sexual touching to rape, were reported across all branches of the military. Based on anonymous surveys of active-duty service members conducted in 2010, however, the Department of Defense says the number of incidents was closer to 19,000.

Women aren't the only ones affected. Of the 65,000 veterans who sought treatment in 2009 for conditions related to military sexual trauma, a term that also includes sexual harassment, 40 percent were men.

“The Invisible War” opens on Friday in theaters in New York, Washington, D.C., Los Angeles and San Francisco in the wake of significant changes to the way the military investigates and handles allegations of sexual assault.

In the past six months, new policies have given victims the right to quickly transfer out of a unit and have access to advocates who will explain the prosecution process. Cases will soon be handled by higher-ranking officers and the Department of Defense has proposed creating special victims units staffed with trained legal personnel.

Critics are encouraged by these policies, but say more needs to be done to deter sexual assault and transform the culture of intimidation and retaliation.

The women, and men, in “The Invisible War,” appear as casualties of that culture.

Kori Cioca, who served in the Coast Guard, said that her chain of command threatened to court-martial her after she reported being raped by a commanding officer in December 2005. The charge, she was told, would be for lying. The officer admitted the attack, but denied the rape. His punishment was 30 days of base restriction and loss of pay. The attack left Cioca with a broken jaw, nerve damage to her face and post-traumatic stress disorder.

Ariana Klay, a first lieutenant in the Marine Corps who served in Iraq, said she was raped by a senior officer and his civilian friend in August 2010. After reporting the assaults, Klay said the subsequent harassment and retaliation led her to attempt suicide. When the Marine Corps investigated her case, Klay was told she had invited harassment by wearing make-up and regulation-length skirts. One of Klay's attackers was court-martialed, but convicted of adultery and indecent language -- not rape.

Trina McDonald, a seaman stationed at a remote naval station in Alaska, said she was repeatedly raped and drugged by members of the military police beginning in 1989. She did not report the assaults since those that were involved in the rapes, including higher-ranking officers, were the individuals to whom she would have reported.

'Inherent conflict of interest'In April, Secretary of Defense Leon Panetta tried to end that dynamic by issuing a directive that the decision to pursue prosecution be handled by a colonel or officer of equivalent rank, a move military officials hope will provide greater accountability.

Previously, a service member’s local unit commander would evaluate the charges and determine whether to pursue disciplinary action -- a system that led to limited prosecutions. Of the 3,192 reports in 2011, only cases on 1,518 subjects were brought forward for disciplinary review last year.

Anu Bhagwati, executive director of the human rights organization Service Women's Action Network and a former captain in the Marine Corps, said that the reluctance of unit commanders to investigate claims is not always based on “malicious attitudes.” Instead, “sometimes there’s just sort of like this misplaced benevolence.” The accused, for example, might have a family and lifelong career, both of which a commander is loath to endanger when it might be difficult to prove an assault. “But what about the victim?” Bhagwati said. “Who’s protecting her?”

Rep. Niki Tsongas, D-Mass, a member of the House Armed Services Committee who has sponsored legislation expanding legal protections for sexual assault victims, told msnbc.com that the move to make high-ranking officers responsible for investigations is an important first step. Without an increase in successful prosecutions, though, Tsongas remains unconvinced that the chain of command should keep its power to determine whether cases are investigated.

Critics, including the filmmakers of “The Invisible War,” believe that the decision to investigate and prosecute must lie completely outside of the chain of command, citing that a colonel may still know or have friendships with the perpetrator or his commander.

“You don’t want to have an inherent conflict of interest where you’re trying to determine if rape occurred,” said Susan Burke, a Washington, D.C., lawyer who has filed a suit on behalf of some of the women who appear in the documentary. Burke would prefer if the decision to shut down rape and sexual assault investigations was made outside of the military by the civilian justice system, or if the chain of command were entirely removed from the process.

Burke’s firm has interviewed more than 400 service members and represents 48 plaintiffs in three different complaints that seek to give service members the right to sue the military for civil damages related to sexual assault.

A 1950 Supreme Court decision prevents service members from bringing torts against the U.S. for injuries sustained during duty, a doctrine Burke said is outdated and was never intended to apply to something like sexual assault. If lawsuits were permitted, Burke believes that would create an institutional deterrent that would ameliorate the underreporting and under-prosecuting of cases.

Even with such recourse, changing the culture around sexual assault in the military will require multiple fronts. “It’s going to have to come from a lot of directions at once,” Tsongas said. “It can't just be from top down or bottom up.”

'We owe it to the public' “The Invisible War﻿﻿” is critical of the military for not doing more to transform that dynamic sooner, focusing in particular on the Department of Defense's Sexual Assault Prevention and Response Office (SAPRO). That unit is charged with overseeing the department's sexual assault policy and providing training and victim-assistance programs.

Until last year, SAPRO's director was a civilian, which critics felt was indicative of the military's lack of urgency around dealing with sexual assault.

Some have criticized the program's training material as too focused on the victim taking responsibility for preventive actions. In the film, a clip from a sexual assault prevention training video portrays a scenario in which a woman is reminded to go out at night with a buddy.

“I was disappointed that film did not accurately portray what SAPRO has done in the past 12 to 18 months,﻿﻿” said Major General Mary Kay Hertog, who was appointed as director in 2011.

Hertog, who called the film “gut-wrenching,” said the office had worked intensely on implementing the new policies, expediting transfers for victims, expanding legal assistance through trained advocates, and developing a standard for document retention so victims can make records available to Veterans Affairs for claims related to an assault.

By October 13, sexual assault response coordinators, which act as a single point of contact for victims, will be credentialed specifically in victim assistance. She said the office was reviewing training materials across the services in order to determine a gold standard. “The training we do is not victim-blaming whatsoever,” she said.

Hertog, who is retiring this month, said she is confident her successor, Major General Gary Patton, will be aggressive in implementing new policies.

The Department of Defense, she said, is committed to investigating perpetrators and removing them from the military: “We owe it to the public to protect their children.”

Rebecca Ruiz is a reporter at msnbc.com and a 2011-2012 Rosalynn Carter Mental Health Journalism Fellow. Follow her on Twitter here.